Table of Contents

Use the following to generate a table of contents... ```{toc} ```

Output:

Bookmarks

You can automatically link back to any piece of text by using the bm inline tag:

• `{bm} LITERAL`, where matches are made using basic case-insensitive text search.
• `{bm} LABEL/REGEX/REGEX_FLAGS`, where matches are made using the regex specified. The regex must have exactly 1 capture group, where the text captured by that group is what gets rendered and gets linked.

The tag can take in either 1 argument or 3 arguments, where forward-slashes (/) are used to delimit arguments. If required, use back-slash to escape the delimiter (e.g. \/).

Usage examples:

• `{bm} coke zero` -- coke zero will be the reference for coke zero, cOkE zErO, and coke zeros.
• `{bm} this text/\b(dog)s?\b/i` -- this text will be the reference for DOG and dog but not doggy, doggo, or ddog.
• `{bm} this text/(carp\w+s?)/` -- this text will be the reference for carps, carpenter, and carpenters, but not carp.
• `{bm} this text/hello\s+(world)/i` -- this text will be the reference for world. Even though the word hello was specified and matched on, it won't be included in the output because it isn't in the capture group.

In certain cases, multiple bookmarks may match a certain piece of text. To resolve this, the bookmark with the longest piece of text captured by the capture group is the one that gets linked to. For example, if the bookmarks Samsung (Galaxy) and Samsung (Galaxy Smartphone) matched on the text Samsung Galaxy Smartphone Holder, the second bookmark would get chosen because capture group 1 returns a longer piece of text.

If the length of the captured text between the matches are equal, an error is thrown and you'll need to find a way to disambiguate. 2 options are available:

1. You can explicitly prevent a piece of text from being matched to any bookmark by wrapping it in a bm-r inline tag (`{bm-ri} TEXT`). For example, coke zero should link to the example above but coke zero won't.
2. You can use the bm-ambiguous inline tag (`{bm-ambiguous} ERROR_TEXT/REGEX/REGEX_FLAGS`) to generate an error telling the user that they need to disambiguate. For example, you may want to create a bookmark for the word base, but in 2 different contexts: base as in pH scale and base as in nitrogenous base. You can use the bm-ambiguous tag to catch any instances of base and throw an error notify the user that they need to provide a more specialized version (e.g. `{bm-ambiguous} Base is too ambiguous. Use either base_pH or base_nucleotide/\b(base)\b/i`), which you can target using normal bm tags (e.g. `{bm} base/\b(base)_nucleotide?\b/i` -- this will match base_nucleotide but only output base).

Notes

Generate notes by using the note block tag:

```{note}
This is a custom note.
```

Output:

TODO: Add CSS styling for this.

Page Title

Set the title of the output document using the title inline/block tag:

```{title}
Markdown Example!
```

Output: (see the title of this HTML page)

If you're using a block tag, make sure you put the title on a NEW line (not on the same line that declares the tag).

MathJax

Add a MathJax TeX expression using mj inline/block tag:

```{mj}
\frac{a}{b}
```

Inline output: $\frac{a}{b}$

Block output:

KaTeX

Add a KaTeX TeX expression using kt inline/block tag:

```{kt}
\frac{a}{b}
```

Inline output: $\frac{a}{b}$

Block output:

GraphViz Diagrams

Generate Graphviz dot diagrams by using dot block tag:

```{dot}
digraph {
  a -> b;
  b -> c;
  b -> d;
}
```

Output:

PlantUML Diagrams

Add a PlantUML diagram using the plantuml block tag:

```{plantuml}
@startuml
class Student {
  Name
}
Student "0..*" - "1..*" Course
(Student, Course) .. Enrollment

class Enrollment {
  drop()
  cancel()
}
@enduml
```

Block output:

CSV

Add a table using the CSV block tag:

```{csv}
!!{ "firstLineHeader": true }
Code,Country
AFG,Afghanistan
ALB,Albania
ALG,Algeria
ASA,American Samoa
AND,Andorra
ANG,Angola
AIA,Anguilla
ATG,Antigua and Barbuda
```

Block output:

GnuPlot Plots

Add a Gnuplot plot using the gnuplot block tag:

```{gnuplot}
set terminal svg size 300,300

a = 0.9
f(x) = a * sin(x)
g(x) = a * cos(x)
# Plot
plot f(x) title 'sin(x)' with lines linestyle 1, \
     g(x) notitle with lines linestyle 2
```

Block output:

Conda (Python)

Add an image or text generated via Python (miniconda) using the conda block tag:

```{conda}
dependencies:
  - python=3.4
----
f = open("/output/text.txt","w+")
f.write("hello world!")
f.close()
```

```{conda}
dependencies:
  - python=3.7
  - matplotlib=3.1
----
import matplotlib.pyplot as plt
plt.plot([1, 2, 3, 4])
plt.ylabel('some numbers')
plt.savefig("/output/out.svg", format="svg")
```

Block output:

hello world!

The Miniconda environment YAML and Python source code are separated by ----. The output produced by the Python script must be a single file written to the /output directory. That file must end in either .txt, .svg, .png, .gif, .jpg, or .jpeg -- the extension defines how the file gets displayed in the final markup.

Standard Markdown

Normal CommonMark features are supported out of the box.

Block Code:

public static void main(String[] args) {
    ...;
}

Inline Code: code

Bold: bold text

Italic: italicized text

Blockquote:

blockquote blockquote blockquote

Ordered List:

1. First item
2. Second item
3. Third item

Unordered List:

• First item
• Second item
• Third item

Horizontal Rule:

Link: Link to Google

Image:

heading2

heading3

heading4

heading5

heading 6

heading 7